582748

Data Structures in Genome Analysis
Data Structures in Genome Analysis
Data Structures in Genome Analysis
582748
5
Bioinformatiikka
Syventävät opinnot
The course covers fundamental data structures that are used for high-throughout sequencing applications in genome analysis. The focus is on Burrows-Wheeler transform -based succinct/compressed index structures for representing, querying, and analyzing collections of DNA sequences. Applications/topics include read alignment, maximal repeat detection, succinct de Bruijn graphs, Lempel-Ziv compression, string kernels, and metagenomics analysis. Prerequisites: Basics of algorithms and data structures. The course follows selected chapters from the textbook Veli Mäkinen, Djamal Belazzougui, Fabio Cunial, and Alexandru I. Tomescu: Genome-Scale Algorithms Design: Biological sequence analysis in the era of high-throughput sequencing. Cambridge University Press. 2015.

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